Bummer, my bad. *That* was a "bug" that I added on purpose to test
the error message; it was not supposed to go live. Please retry again
now (now I've done my homework and verified it on my computer).
# In a fresh R session:
source("http://www.braju.com/R/hbLite.R";);
hbInstallPackages2("BRAJU:aroma.core", force=TRUE, verbose=TRUE, debug=TRUE);
/Henrik
On Thu, Nov 12, 2009 at 3:42 PM, anitaKCL <[email protected]> wrote:
> Hi Henrik,
>
> No luck.
> This is the error which I get:
>
> > source("http://www.braju.com/R/hbLite.R";);
> > hbInstallPackages2("BRAJU:aroma.core", force=TRUE, verbose=TRUE,
> debug=TRUE);
> Installing/updating: BRAJU:aroma.core
> Repositories: BRAJU
> Package: aroma.core
> Tags:
> If installation/update of package 'aroma.core' is needed, it is
> enforced to be from source. The most likely reason for this is that
> the repository does currently not contain a prebuild binary version
> for Mac (or for the type 'mac.binary.leopard' requested).
> Updating packages: aroma.core from repository 'http://www.braju.com/R/repos'
> 01/01. aroma.core: missing. Installing:
> ERROR: Failed to install package: aroma.core
> <simpleError in doTryCatch(return(expr), name, parentenv, handler):
> object 'sspkg' not found>
> traceback():
> No traceback available
> NULL
> Call:
> List of 1
> $ contriburl: chr "http://www.braju.com/R/repos";
> >
>
> thanks a lot for your help,
>
> Anita
>
>
> On 12 Nov 2009, at 12:59 PM, Henrik Bengtsson wrote:
>
>> Hi,
>>
>> no, you don't have to remove anything at all. FYI, there is nothing
>> magic (unfortunately) going on when install aroma.* et al packages.
>> This is the same case when you use biocLite() to install those
>> packages. I just have wrapper functions that do all the messy work
>> for you. Internally install.packages() with the correct arguments are
>> called. To me it does not look like it has anything to do with my
>> installation functions, but a mishaps in the OSX 64-bit build(?) used
>> here. This is what I am trying to narrow down now and hopeful can
>> find a workaround for and report to R-devel to get fixed.
>>
>> Since I don't have access R on OSX 64-bit, I rely on you (any OSX
>> 64-bit user will be useful). Could you please try the following and
>> report what the (long) output it (you need restart R):
>>
>> source("http://www.braju.com/R/hbLite.R";);
>> hbInstallPackages2("BRAJU:aroma.core", force=TRUE, verbose=TRUE,
>> debug=TRUE);
>>
>> /Henrik
>>
>> On Thu, Nov 12, 2009 at 11:22 AM, Anita
>> <[email protected]> wrote:
>>> Dear Henrik,
>>>
>>> Unfortunately, I still have the same issues:
>>> If installation/update of package 'aroma.core (>= 1.3.1)' is needed,
>>> it is enforced to be from source. The most likely reason for this is
>>> that the repository does currently not contain a prebuild binary
>>> version for Mac (or for the type 'mac.binary.leopard' requested).
>>> Updating packages: aroma.core from repository 'http://www.braju.com/
>>> R/
>>> repos'
>>> 01/01. aroma.core: missing. Installing:
>>> <simpleError: invalid version specification 1.6.5NA>
>>> Installing/updating: BRAJU:aroma.affymetrix (>= 1.3.0)
>>> Repositories: BRAJU
>>> Package: aroma.affymetrix (>= 1.3.0)
>>> Tags:
>>> If installation/update of package 'aroma.affymetrix (>= 1.3.0)' is
>>> needed, it is enforced to be from source. The most likely reason for
>>> this is that the repository does currently not contain a prebuild
>>> binary version for Mac (or for the type 'mac.binary.leopard'
>>> requested).
>>> Updating packages: aroma.affymetrix from repository 'http://
>>> www.braju.com/R/repos'
>>> 01/01. aroma.affymetrix: missing. Installing:
>>> <simpleError: invalid version specification 1.2.4NA>
>>>
>>> AND
>>>
>>> If installation/update of package 'sfit (>= 0.1.5)' is needed, it is
>>> enforced to be from source. The most likely reason for this is that
>>> the repository does currently not contain a prebuild binary version
>>> for Mac (or for the type 'mac.binary.leopard' requested).
>>> Updating packages: sfit from repository 'http://www.braju.com/R/
>>> repos'
>>> 01/01. sfit: v0.1.8, i.e. up to date.
>>> Installing/updating: RFORGE:gsmoothr (>= 0.1.3)
>>> Repositories: RFORGE
>>> Package: gsmoothr (>= 0.1.3)
>>> Tags:
>>> Warning: unable to access index for repository
>>> http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.9
>>> Updating packages: gsmoothr from repository 'http://R-Forge.R-
>>> project.org/bin/macosx/leopard/contrib/2.9'
>>> 01/01. gsmoothr: not available.
>>>
>>> Do I need to remove anything before I try to install it again.
>>>
>>> Many thanks for your help,
>>>
>>> Anita
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run
>>> the latest version of the package, 2) to report the output of
>>> sessionInfo() and traceback(), and 3) to post a complete code
>>> example.
>>>
>>>
>>> You received this message because you are subscribed to the Google
>>> Groups "aroma.affymetrix" group.
>>> To post to this group, send email to aroma-
>>> [email protected]
>>> To unsubscribe from this group, send email to
>>> [email protected]
>>> For more options, visit this group at
>>> http://groups.google.com/group/aroma-affymetrix?hl=en
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of
>> sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
>> Groups "aroma.affymetrix" group.
>> To post to this group, send email to [email protected]
>> To unsubscribe from this group, send email to
>> [email protected]
>> For more options, visit this group at
>> http://groups.google.com/group/aroma-affymetrix?hl=en
>
> ----------------------------------------------------------
> Dr Anita Grigoriadis
> Breakthrough Breast Research Unit
> Research Oncology
> 3rd Floor
> Bermondsey Wing
> Guy's Hospital
> Great Maze Pond
> London, SE1 9RT
>
> Tel: 020 7188 7188 ext.51093
> Fax: 020 7188 3666
> [email protected]
> [email protected]
>
> ----------------------------------------------------------
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To post to this group, send email to [email protected]
> To unsubscribe from this group, send email to
> [email protected]
> For more options, visit this group at
> http://groups.google.com/group/aroma-affymetrix?hl=en
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
